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[matrix] Diff of /pkg/Matrix/src/Csparse.c
 [matrix] / pkg / Matrix / src / Csparse.c

Diff of /pkg/Matrix/src/Csparse.c

pkg/src/Csparse.c revision 1657, Wed Nov 1 16:29:53 2006 UTC pkg/Matrix/src/Csparse.c revision 2834, Mon Sep 3 10:30:03 2012 UTC
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1                          /* Sparse matrices in compressed column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2
3  #include "Csparse.h"  #include "Csparse.h"
4    #include "Tsparse.h"
5  #include "chm_common.h"  #include "chm_common.h"
6
7  SEXP Csparse_validate(SEXP x)  /** "Cheap" C version of  Csparse_validate() - *not* sorting : */
8    Rboolean isValid_Csparse(SEXP x)
9  {  {
10      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
11      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
12          islot = GET_SLOT(x, Matrix_iSym);          islot = GET_SLOT(x, Matrix_iSym);
13      int j, k, ncol, nrow, sorted,      int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
14            nrow = dims[0],
15            ncol = dims[1],
16            *xp = INTEGER(pslot),
17            *xi = INTEGER(islot);
18
19        if (length(pslot) != dims[1] + 1)
20            return FALSE;
21        if (xp[0] != 0)
22            return FALSE;
23        if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24            return FALSE;
25        for (j = 0; j < xp[ncol]; j++) {
26            if (xi[j] < 0 || xi[j] >= nrow)
27                return FALSE;
28        }
29        for (j = 0; j < ncol; j++) {
30            if (xp[j] > xp[j + 1])
31                return FALSE;
32        }
33        return TRUE;
34    }
35
36    SEXP Csparse_validate(SEXP x) {
37        return Csparse_validate_(x, FALSE);
38    }
39
40    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
41        return Csparse_validate_(x, asLogical(maybe_modify));
42    }
43
44    SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)
45    {
46        /* NB: we do *NOT* check a potential 'x' slot here, at all */
47        SEXP pslot = GET_SLOT(x, Matrix_pSym),
48            islot = GET_SLOT(x, Matrix_iSym);
49        Rboolean sorted, strictly;
50        int j, k,
51          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
52            nrow = dims[0],
53            ncol = dims[1],
54          *xp = INTEGER(pslot),          *xp = INTEGER(pslot),
55          *xi = INTEGER(islot);          *xi = INTEGER(islot);
56
nrow = dims[0];
ncol = dims[1];
57      if (length(pslot) != dims[1] + 1)      if (length(pslot) != dims[1] + 1)
58          return mkString(_("slot p must have length = ncol(.) + 1"));          return mkString(_("slot p must have length = ncol(.) + 1"));
59      if (xp[0] != 0)      if (xp[0] != 0)
60          return mkString(_("first element of slot p must be zero"));          return mkString(_("first element of slot p must be zero"));
61      if (length(islot) != xp[ncol])      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
62          return          return
63              mkString(_("last element of slot p must match length of slots i and x"));              mkString(_("last element of slot p must match length of slots i and x"));
64      for (j = 0; j < length(islot); j++) {      for (j = 0; j < xp[ncol]; j++) {
65          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
66              return mkString(_("all row indices must be between 0 and nrow-1"));              return mkString(_("all row indices must be between 0 and nrow-1"));
67      }      }
68      sorted = TRUE;      sorted = TRUE; strictly = TRUE;
69      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
70          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
71              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
72          for (k = xp[j] + 1; k < xp[j + 1]; k++)          if(sorted) /* only act if >= 2 entries in column j : */
73              if (xi[k] < xi[k - 1]) sorted = FALSE;              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
74                    if (xi[k] < xi[k - 1])
75                        sorted = FALSE;
76                    else if (xi[k] == xi[k - 1])
77                        strictly = FALSE;
78                }
79      }      }
80      if (!sorted) {      if (!sorted) {
81          cholmod_sparse *chx = as_cholmod_sparse(x);          if(maybe_modify) {
82          cholmod_sort(chx, &c);              CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
83          Free(chx);              R_CheckStack();
84                as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
85                /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
86
87                /* Now re-check that row indices are *strictly* increasing
88                 * (and not just increasing) within each column : */
89                for (j = 0; j < ncol; j++) {
90                    for (k = xp[j] + 1; k < xp[j + 1]; k++)
91                        if (xi[k] == xi[k - 1])
92                            return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));
93                }
94            } else { /* no modifying sorting : */
95                return mkString(_("row indices are not sorted within columns"));
96            }
97        } else if(!strictly) {  /* sorted, but not strictly */
98            return mkString(_("slot i is not *strictly* increasing inside a column"));
99      }      }
100      return ScalarLogical(1);      return ScalarLogical(1);
101  }  }
102
103    SEXP Rsparse_validate(SEXP x)
104    {
105        /* NB: we do *NOT* check a potential 'x' slot here, at all */
106        SEXP pslot = GET_SLOT(x, Matrix_pSym),
107            jslot = GET_SLOT(x, Matrix_jSym);
108        Rboolean sorted, strictly;
109        int i, k,
110            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
111            nrow = dims[0],
112            ncol = dims[1],
113            *xp = INTEGER(pslot),
114            *xj = INTEGER(jslot);
115
116        if (length(pslot) != dims[0] + 1)
117            return mkString(_("slot p must have length = nrow(.) + 1"));
118        if (xp[0] != 0)
119            return mkString(_("first element of slot p must be zero"));
120        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
121            return
122                mkString(_("last element of slot p must match length of slots j and x"));
123        for (i = 0; i < length(jslot); i++) {
124            if (xj[i] < 0 || xj[i] >= ncol)
125                return mkString(_("all column indices must be between 0 and ncol-1"));
126        }
127        sorted = TRUE; strictly = TRUE;
128        for (i = 0; i < nrow; i++) {
129            if (xp[i] > xp[i+1])
130                return mkString(_("slot p must be non-decreasing"));
131            if(sorted)
132                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
133                    if (xj[k] < xj[k - 1])
134                        sorted = FALSE;
135                    else if (xj[k] == xj[k - 1])
136                        strictly = FALSE;
137                }
138        }
139        if (!sorted)
140            /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
141            return mkString(_("slot j is not increasing inside a column"));
142        else if(!strictly) /* sorted, but not strictly */
143            return mkString(_("slot j is not *strictly* increasing inside a column"));
144
145        return ScalarLogical(1);
146    }
147
148
149    /* Called from ../R/Csparse.R : */
150    /* Can only return [dln]geMatrix (no symm/triang);
151     * FIXME: replace by non-CHOLMOD code ! */
152  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
153  {  {
154      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
155      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      /* This loses the symmetry property, since cholmod_dense has none,
156         * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
157         * to numeric (CHOLMOD_REAL) ones : */
158        CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
159        int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
160        R_CheckStack();
161
162      Free(chxs);      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
return chm_dense_to_SEXP(chxd, 1, Real_kind(x));
163  }  }
164
165    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
166  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
167  {  {
168      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
169      cholmod_sparse      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
170          *chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      int tr = asLogical(tri);
171      int uploT = 0; char *diag = "";      R_CheckStack();
172
173      Free(chxs);      return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
174      if (asLogical(tri)) {       /* triangular sparse matrices */                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
175          uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?                                0, tr ? diag_P(x) : "",
-1 : 1;
diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));
}
return chm_sparse_to_SEXP(chxcp, 1, uploT, 0, diag,
176                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
177  }  }
178
179  SEXP Csparse_to_matrix(SEXP x)  // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
180    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
181    {
182        return nz2Csparse(x, asInteger(res_kind));
183    }
184    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
185    SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
186  {  {
187      cholmod_sparse *chxs = as_cholmod_sparse(x);      const char *cl_x = class_P(x);
188      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
189        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
190        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
191        SEXP ans;
192        char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
193        strcpy(ncl, cl_x);
194        double *dx_x; int *ix_x;
195        ncl[0] = (r_kind == x_double ? 'd' :
196                  (r_kind == x_logical ? 'l' :
197                   /* else (for now):  r_kind == x_integer : */ 'i'));
198        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
199        // create a correct 'x' slot:
200        switch(r_kind) {
201            int i;
202        case x_double: // 'd'
203            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
204            for (i=0; i < nnz; i++) dx_x[i] = 1.;
205            break;
206        case x_logical: // 'l'
207            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
208            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
209            break;
210        case x_integer: // 'i'
211            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
212            for (i=0; i < nnz; i++) ix_x[i] = 1;
213            break;
214
215        default:
216            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
217                  r_kind);
218        }
219
220        // now copy all other slots :
221        slot_dup(ans, x, Matrix_iSym);
222        slot_dup(ans, x, Matrix_pSym);
223        slot_dup(ans, x, Matrix_DimSym);
224        slot_dup(ans, x, Matrix_DimNamesSym);
225        if(ncl[1] != 'g') { // symmetric or triangular ...
226            slot_dup_if_has(ans, x, Matrix_uploSym);
227            slot_dup_if_has(ans, x, Matrix_diagSym);
228        }
229        UNPROTECT(1);
230        return ans;
231    }
232
233      Free(chxs);  SEXP Csparse_to_matrix(SEXP x)
234      return chm_dense_to_matrix(chxd, 1,  {
235                                 GET_SLOT(x, Matrix_DimNamesSym));      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
236                                   1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
237  }  }
238
239  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
240  {  {
241      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
242      cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
243      int uploT = 0;      int tr = asLogical(tri);
244      char *diag = "";      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
245      int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      R_CheckStack();
246
247      Free(chxs);      return chm_triplet_to_SEXP(chxt, 1,
248      if (asLogical(tri)) {       /* triangular sparse matrices */                                 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
249          uploT = (*uplo_P(x) == 'U') ? -1 : 1;                                 Rkind, tr ? diag_P(x) : "",
diag = diag_P(x);
}
return chm_triplet_to_SEXP(chxt, 1, uploT, Rkind, diag,
250                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
251  }  }
252
253  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
254  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
255  {  {
256      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
257      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
258        R_CheckStack();
259
260      if (!(chx->stype))      if (!(chx->stype))
261          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
262      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
263      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
Free(chx);
264      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
265                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
266  }  }
267
268  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
269  {  {
270      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
271      int uploT = (*CHAR(asChar(uplo)) == 'U') ? -1 : 1;      if(n != adims[1]) {
272      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;          error(_("Csparse_general_to_symmetric(): matrix is not square!"));
273            return R_NilValue; /* -Wall */
274        }
275        CHM_SP chx = AS_CHM_SP__(x), chgx;
276        int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
277        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
278        R_CheckStack();
279      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
280      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
Free(chx);
281      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
282                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
283  }  }
284
285  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
286  {  {
287      cholmod_sparse *chx = as_cholmod_sparse(x);      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
288      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;       *       since cholmod (& cs) lacks sparse 'int' matrices */
289      cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);      CHM_SP chx = AS_CHM_SP__(x);
290        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
291        CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
292      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
293      int uploT = 0; char *diag = "";      int tr = asLogical(tri);
294        R_CheckStack();
295
Free(chx);
296      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
297      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
298      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
299      UNPROTECT(1);      UNPROTECT(1);
300      if (asLogical(tri)) {       /* triangular sparse matrices */      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
301          uploT = (*uplo_P(x) == 'U') ? -1 : 1;                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
302          diag = diag_P(x);                                Rkind, tr ? diag_P(x) : "", dn);
}
return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);
303  }  }
304
305  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
306  {  {
307      cholmod_sparse *cha = as_cholmod_sparse(a),      CHM_SP
308          *chb = as_cholmod_sparse(b);          cha = AS_CHM_SP(a),
309      cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          chb = AS_CHM_SP(b),
310      SEXP dn = allocVector(VECSXP, 2);          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
311                                   /* values:= is_numeric (T/F) */ cha->xtype > 0,
312                                   /*out sorted:*/ 1, &c);
313        const char *cl_a = class_P(a), *cl_b = class_P(b);
314        char diag[] = {'\0', '\0'};
315        int uploT = 0;
316        SEXP dn = PROTECT(allocVector(VECSXP, 2));
317        R_CheckStack();
318
319      Free(cha); Free(chb);  #ifdef DEBUG_Matrix_verbose
320        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
321    #endif
322
323        /* Preserve triangularity and even unit-triangularity if appropriate.
324         * Note that in that case, the multiplication itself should happen
325         * faster.  But there's no support for that in CHOLMOD */
326
327        /* UGLY hack -- rather should have (fast!) C-level version of
328         *       is(a, "triangularMatrix") etc */
329        if (cl_a[1] == 't' && cl_b[1] == 't')
330            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
331            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
332                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
333                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
334                    /* "remove the diagonal entries": */
335                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
336                    diag[0]= 'U';
337                }
338                else diag[0]= 'N';
339            }
340      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
341                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
342      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
343                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
344      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
345        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
346  }  }
347
348  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
349  {  {
350      cholmod_sparse *cha = as_cholmod_sparse(a),      int tr = asLogical(trans);
351          *chb = as_cholmod_sparse(b);      CHM_SP
352      cholmod_sparse *chta = cholmod_transpose(cha, 1, &c);          cha = AS_CHM_SP(a),
353      cholmod_sparse *chc = cholmod_ssmult(chta, chb, 0, cha->xtype, 1, &c);          chb = AS_CHM_SP(b),
354      SEXP dn = allocVector(VECSXP, 2);          chTr, chc;
355        const char *cl_a = class_P(a), *cl_b = class_P(b);
356        char diag[] = {'\0', '\0'};
357        int uploT = 0;
358        SEXP dn = PROTECT(allocVector(VECSXP, 2));
359        R_CheckStack();
360
361      Free(cha); Free(chb); cholmod_free_sparse(&chta, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
362        chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
363                             /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
364        cholmod_free_sparse(&chTr, &c);
365
366        /* Preserve triangularity and unit-triangularity if appropriate;
367         * see Csparse_Csparse_prod() for comments */
368        if (cl_a[1] == 't' && cl_b[1] == 't')
369            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
370                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
371                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
372                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
373                    diag[0]= 'U';
374                }
375                else diag[0]= 'N';
376            }
377      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
378                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
379      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
380                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
381      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
382        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
383  }  }
384
385  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
386  {  {
387      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
388      cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
389      cholmod_dense *chc =      CHM_DN chb = AS_CHM_DN(b_M);
390          cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
391      double alpha[] = {1,0}, beta[] = {0,0};                                          chb->xtype, &c);
392        SEXP dn = PROTECT(allocVector(VECSXP, 2));
393      cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);      double one[] = {1,0}, zero[] = {0,0};
394      Free(cha); Free(chb);      int nprot = 2;
395      UNPROTECT(1);      R_CheckStack();
396      return chm_dense_to_SEXP(chc, 1, 0);      /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
397        if(cha->xtype == CHOLMOD_PATTERN) {
398            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
399            /*        " --> slightly inefficient coercion")); */
400
401            // This *fails* to produce a CHOLMOD_REAL ..
402            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
403            // --> use our Matrix-classes
404            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
405            cha = AS_CHM_SP(da);
406        }
407        cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
408        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
409                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
410        SET_VECTOR_ELT(dn, 1,
411                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
412        UNPROTECT(nprot);
413        return chm_dense_to_SEXP(chc, 1, 0, dn);
414  }  }
415
416  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
417  {  {
418      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
419      cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
420      cholmod_dense *chc =      CHM_DN chb = AS_CHM_DN(b_M);
421          cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
422      double alpha[] = {1,0}, beta[] = {0,0};                                          chb->xtype, &c);
423        SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
424      cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);      double one[] = {1,0}, zero[] = {0,0};
425      Free(cha); Free(chb);      R_CheckStack();
426      UNPROTECT(1);      // -- see Csparse_dense_prod() above :
427      return chm_dense_to_SEXP(chc, 1, 0);      if(cha->xtype == CHOLMOD_PATTERN) {
428            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
429            cha = AS_CHM_SP(da);
430        }
431        cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
432        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
433                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
434        SET_VECTOR_ELT(dn, 1,
435                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
436        UNPROTECT(nprot);
437        return chm_dense_to_SEXP(chc, 1, 0, dn);
438  }  }
439
440    /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
441       see Csparse_Csparse_crossprod above for  x'y and x y' */
442  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
443  {  {
444      int trip = asLogical(triplet),      int trip = asLogical(triplet),
445          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
446      cholmod_triplet  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
447          *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
448      cholmod_sparse *chcp, *chxt,  #else /* workaround needed:*/
449          *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)      SEXP xx = PROTECT(Tsparse_diagU2N(x));
450          : as_cholmod_sparse(x);      CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
451    #endif
452        CHM_SP chcp, chxt,
453            chx = (trip ?
454                   cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
455                   AS_CHM_SP(x));
456      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
457        R_CheckStack();
458
459      if (!tr)      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
chxt = cholmod_transpose(chx, chx->xtype, &c);
460      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
461      if(!chcp)      if(!chcp) {
462            UNPROTECT(1);
463          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
464        }
465      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
466      chcp->stype = 1;      chcp->stype = 1;
467      if (trip) {      if (trip) cholmod_free_sparse(&chx, &c);
cholmod_free_sparse(&chx, &c);
Free(cht);
} else {
Free(chx);
}
468      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
469                                  /* create dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
SET_VECTOR_ELT(dn, 0,
470                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
471                                          (tr) ? 1 : 0)));                                          (tr) ? 0 : 1)));
472      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
473    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
474      UNPROTECT(1);      UNPROTECT(1);
475    #else
476        UNPROTECT(2);
477    #endif
478      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
479  }  }
480
481    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
482    *  at least all "explicit" zeros */
483  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
484  {  {
485      cholmod_sparse *chx = as_cholmod_sparse(x),      const char *cl = class_P(x);
486          *ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
487        int tr = (cl[1] == 't');
488        CHM_SP chx = AS_CHM_SP__(x);
489        CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
490      double dtol = asReal(tol);      double dtol = asReal(tol);
491      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
492        R_CheckStack();
493
494      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
495          error(_("cholmod_drop() failed"));          error(_("cholmod_drop() failed"));
496      Free(chx);     return chm_sparse_to_SEXP(ans, 1,
497      /* FIXME: currently drops dimnames */                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
498      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);                                Rkind, tr ? diag_P(x) : "",
499                                  GET_SLOT(x, Matrix_DimNamesSym));
500  }  }
501

502  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
503  {  {
504      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
505          *chy = as_cholmod_sparse(y), *ans;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
506      int Rkind = 0; /* only for "d" - FIXME */          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
507            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
508      ans = cholmod_horzcat(chx, chy, 1, &c);      R_CheckStack();
509      Free(chx); Free(chy);
510      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
511      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
512                                  1, 0, Rkind, "", R_NilValue);
513  }  }
514
515  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
516  {  {
517      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
518          *chy = as_cholmod_sparse(y), *ans;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
519      int Rkind = 0; /* only for "d" - FIXME */          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
520            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
521      ans = cholmod_vertcat(chx, chy, 1, &c);      R_CheckStack();
522      Free(chx); Free(chy);
523      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
524      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
525                                  1, 0, Rkind, "", R_NilValue);
526  }  }
527
528  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
529  {  {
530      cholmod_sparse *chx = as_cholmod_sparse(x), *ans;      CHM_SP chx = AS_CHM_SP__(x);
531      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
532        CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
533        R_CheckStack();
534
535      ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
536      Free(chx);                                GET_SLOT(x, Matrix_DimNamesSym));
return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
537  }  }
538
539  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
540  {  {
541      cholmod_sparse *chx = as_cholmod_sparse(x);      const char *cl = class_P(x);
542      cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
543        if (cl[1] != 't' || *diag_P(x) != 'U') {
544            /* "trivially fast" when not triangular (<==> no 'diag' slot),
545               or not *unit* triangular */
546            return (x);
547        }
548        else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
549            CHM_SP chx = AS_CHM_SP__(x);
550            CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
551      double one[] = {1, 0};      double one[] = {1, 0};
552      cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
553      int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
554          -1 : 1;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
555
556      Free(chx); cholmod_free_sparse(&eye, &c);          R_CheckStack();
557            cholmod_free_sparse(&eye, &c);
558      return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",      return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
559                                duplicate(GET_SLOT(x, Matrix_DimNamesSym)));                                    GET_SLOT(x, Matrix_DimNamesSym));
560        }
561    }
562
563    SEXP Csparse_diagN2U(SEXP x)
564    {
565        const char *cl = class_P(x);
566        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
567        if (cl[1] != 't' || *diag_P(x) != 'N') {
568            /* "trivially fast" when not triangular (<==> no 'diag' slot),
569               or already *unit* triangular */
570            return (x);
571        }
572        else { /* triangular with diag='N'): now drop the diagonal */
573            /* duplicate, since chx will be modified: */
574            SEXP xx = PROTECT(duplicate(x));
575            CHM_SP chx = AS_CHM_SP__(xx);
576            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
577                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
578            R_CheckStack();
579
580            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
581
582            SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
583                                          uploT, Rkind, "U",
584                                          GET_SLOT(x, Matrix_DimNamesSym));
585            UNPROTECT(1);// only now !
586            return ans;
587        }
588  }  }
589
590    /**
591     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
592     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
593     * @param x CsparseMatrix
594     * @param i row     indices (0-origin), or NULL (R's)
595     * @param j columns indices (0-origin), or NULL
596     *
597     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
598     */
599  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
600  {  {
601      cholmod_sparse *chx = as_cholmod_sparse(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
602      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
603          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
604      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
605        R_CheckStack();
606
607      if (rsize >= 0 && !isInteger(i))      if (rsize >= 0 && !isInteger(i))
608          error(_("Index i must be NULL or integer"));          error(_("Index i must be NULL or integer"));
609      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
610          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
611      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
612                                                  INTEGER(j), csize,      if (!chx->stype) {/* non-symmetric Matrix */
613            return chm_sparse_to_SEXP(cholmod_submatrix(chx,
614                                                        (rsize < 0) ? NULL : INTEGER(i), rsize,
615                                                        (csize < 0) ? NULL : INTEGER(j), csize,
616                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
617                                1, 0, Rkind, "", R_NilValue);                                    1, 0, Rkind, "",
618                                      /* FIXME: drops dimnames */ R_NilValue);
619        }
620                                    /* for now, cholmod_submatrix() only accepts "generalMatrix" */
621        CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
622        CHM_SP ans = cholmod_submatrix(tmp,
623                                       (rsize < 0) ? NULL : INTEGER(i), rsize,
624                                       (csize < 0) ? NULL : INTEGER(j), csize,
625                                       TRUE, TRUE, &c);
626        cholmod_free_sparse(&tmp, &c);
627        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
628    }
629
630    #define _d_Csp_
631    #include "t_Csparse_subassign.c"
632
633    #define _l_Csp_
634    #include "t_Csparse_subassign.c"
635
636    #define _i_Csp_
637    #include "t_Csparse_subassign.c"
638
639    #define _n_Csp_
640    #include "t_Csparse_subassign.c"
641
642    #define _z_Csp_
643    #include "t_Csparse_subassign.c"
644
645
646
647    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
648    {
649        FILE *f = fopen(CHAR(asChar(fname)), "w");
650
651        if (!f)
652            error(_("failure to open file \"%s\" for writing"),
653                  CHAR(asChar(fname)));
654        if (!cholmod_write_sparse(f, AS_CHM_SP(x),
655                                  (CHM_SP)NULL, (char*) NULL, &c))
656            error(_("cholmod_write_sparse returned error code"));
657        fclose(f);
658        return R_NilValue;
659    }
660
661
662    /**
663     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
664     * cholmod_sparse factor (LDL = TRUE).
665     *
666     * @param n  dimension of the matrix.
667     * @param x_p  'p' (column pointer) slot contents
668     * @param x_x  'x' (non-zero entries) slot contents
669     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
670     * @param resultKind a (SEXP) string indicating which kind of result is desired.
671     *
672     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
673     */
674    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
675    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
676    {
677        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
678        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
679        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
680                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
681                       ((!strcmp(res_ch, "prod")) ? prod :
682                        ((!strcmp(res_ch, "diag")) ? diag :
683                         ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
684                          -1)))));
685        int i, n_x, i_from = 0;
686        SEXP ans = PROTECT(allocVector(REALSXP,
687    /*                                 ^^^^  FIXME[Generalize] */
688                                       (res_kind == diag ||
689                                        res_kind == diag_backpermuted) ? n : 1));
690        double *v = REAL(ans);
691    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
692
693    #define for_DIAG(v_ASSIGN)                                      \
694        for(i = 0; i < n; i++, i_from += n_x) {                     \
695            /* looking at i-th column */                            \
696            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
697            v_ASSIGN;                                               \
698        }
699
700        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
701         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
702         *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
703         *            where nx = (x_p[i+1] - x_p[i])
704         */
705
706        switch(res_kind) {
707        case trace:
708            v[0] = 0.;
709            for_DIAG(v[0] += x_x[i_from]);
710            break;
711
712        case sum_log:
713            v[0] = 0.;
714            for_DIAG(v[0] += log(x_x[i_from]));
715            break;
716
717        case prod:
718            v[0] = 1.;
719            for_DIAG(v[0] *= x_x[i_from]);
720            break;
721
722        case diag:
723            for_DIAG(v[i] = x_x[i_from]);
724            break;
725
726        case diag_backpermuted:
727            for_DIAG(v[i] = x_x[i_from]);
728
729            warning(_("%s = '%s' (back-permuted) is experimental"),
730                    "resultKind", "diagBack");
731            /* now back_permute : */
732            for(i = 0; i < n; i++) {
733                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
734                /*^^^^ FIXME[Generalize] */
735            }
736            break;
737
738        default: /* -1 from above */
739            error(_("diag_tC(): invalid 'resultKind'"));
740            /* Wall: */ ans = R_NilValue; v = REAL(ans);
741        }
742
743        UNPROTECT(1);
744        return ans;
745    }
746
747    /**
748     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
749     * cholmod_sparse factor (LDL = TRUE).
750     *
751     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
752     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
753     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
754     *                   only used for "diagBack"
755     * @param resultKind a (SEXP) string indicating which kind of result is desired.
756     *
757     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
758     */
759    SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
760    {
761        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
762            *x_p  = INTEGER(pslot),
763            *perm = INTEGER(perm_slot);
764        double *x_x = REAL(xslot);
765    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
766
767        return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
768    }
769
770    /**
771     * Create a Csparse matrix object from indices and/or pointers.
772     *
773     * @param cls name of actual class of object to create
774     * @param i optional integer vector of length nnz of row indices
775     * @param j optional integer vector of length nnz of column indices
776     * @param p optional integer vector of length np of row or column pointers
777     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
778     * @param x optional vector of values
779     * @param nnz length of vectors i, j and/or x, whichever is to be used
780     * @param dims optional integer vector of length 2 to be used as
781     *     dimensions.  If dims == (int*)NULL then the maximum row and column
782     *     index are used as the dimensions.
783     * @param dimnames optional list of length 2 to be used as dimnames
784     * @param index1 indicator of 1-based indices
785     *
786     * @return an SEXP of class cls inheriting from CsparseMatrix.
787     */
788    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
789                        void* x, int nnz, int* dims, SEXP dimnames,
790                        int index1)
791    {
792        SEXP ans;
793        int *ij = (int*)NULL, *tri, *trj,
794            mi, mj, mp, nrow = -1, ncol = -1;
795        int xtype = -1;             /* -Wall */
796        CHM_TR T;
797        CHM_SP A;
798
799        if (np < 0 || nnz < 0)
800            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
801                  np, nnz);
802        if (1 != ((mi = (i == (int*)NULL)) +
803                  (mj = (j == (int*)NULL)) +
804                  (mp = (p == (int*)NULL))))
805            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
806        if (mp) {
807            if (np) error(_("np = %d, must be zero when p is NULL"), np);
808        } else {
809            if (np) {               /* Expand p to form i or j */
810                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
811                for (int ii = 0; ii < np; ii++)
812                    if (p[ii] > p[ii + 1])
813                        error(_("p must be non-decreasing"));
814                if (p[np] != nnz)
815                    error("p[np] = %d != nnz = %d", p[np], nnz);
816                ij = Calloc(nnz, int);
817                if (mi) {
818                    i = ij;
819                    nrow = np;
820                } else {
821                    j = ij;
822                    ncol = np;
823                }
824                /* Expand p to 0-based indices */
825                for (int ii = 0; ii < np; ii++)
826                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
827            } else {
828                if (nnz)
829                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
830                          nnz);
831            }
832        }
833        /* calculate nrow and ncol */
834        if (nrow < 0) {
835            for (int ii = 0; ii < nnz; ii++) {
836                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
837                if (i1 < 1) error(_("invalid row index at position %d"), ii);
838                if (i1 > nrow) nrow = i1;
839            }
840        }
841        if (ncol < 0) {
842            for (int jj = 0; jj < nnz; jj++) {
843                int j1 = j[jj] + (index1 ? 0 : 1);
844                if (j1 < 1) error(_("invalid column index at position %d"), jj);
845                if (j1 > ncol) ncol = j1;
846            }
847        }
848        if (dims != (int*)NULL) {
849            if (dims[0] > nrow) nrow = dims[0];
850            if (dims[1] > ncol) ncol = dims[1];
851        }
852        /* check the class name */
853        if (strlen(cls) != 8)
854            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
855        if (!strcmp(cls + 2, "CMatrix"))
856            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
857        switch(cls[0]) {
858        case 'd':
859        case 'l':
860            xtype = CHOLMOD_REAL;
861        break;
862        case 'n':
863            xtype = CHOLMOD_PATTERN;
864            break;
865        default:
866            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
867        }
868        if (cls[1] != 'g')
869            error(_("Only 'g'eneral sparse matrix types allowed"));
870        /* allocate and populate the triplet */
871        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
872                                     xtype, &c);
873        T->x = x;
874        tri = (int*)T->i;
875        trj = (int*)T->j;
876        for (int ii = 0; ii < nnz; ii++) {
877            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
878            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
879        }
880        /* create the cholmod_sparse structure */
881        A = cholmod_triplet_to_sparse(T, nnz, &c);
882        cholmod_free_triplet(&T, &c);
883        /* copy the information to the SEXP */
884        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
885    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
886        /* allocate and copy common slots */
887        nnz = cholmod_nnz(A, &c);
888        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
889        dims[0] = A->nrow; dims[1] = A->ncol;
890        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
891        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
892        switch(cls[1]) {
893        case 'd':
894            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
895            break;
896        case 'l':
897            error(_("code not yet written for cls = \"lgCMatrix\""));
898        }
899    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
900        cholmod_free_sparse(&A, &c);
901        UNPROTECT(1);
902        return ans;
903  }  }

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